Thanks Jason last time I interprate it wrongly so that time I did,nt get, now it
is clear to me.
Thanks once again.
> On Wed, Jun 16, 2010 at 2:55 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I am doing pH based conformational study.
>>
>> I have prepared CPIN file there is by default protonation state is 0 for
>> side chain
>> of titratable residues.During generation of this file I havent specify the
>> protonation state.
>>
>> Should I modifify the protonation state before doing MD simulation or I can
>> proceed,
>> If is it so then why?
>>
>>
>> Whatever I got from manual that during Md simulation diffrent ptonation
>> state is
>> sample out by each MC sampling step.
>>
>> So should I left initial protonation state 0 or chang it.
>> Can anybody please explain this.
>>
>
> That is what I attempted to do with my previous email. It is unlikely that
> you have to change it, and you may only have to if there are a couple of
> carboxylates that are closely interacting (making it obvious that not both
> can be charged). This may cause the system to blow up... but it's
> unlikely. Just make sure that each time you restart a simulation, use the
> cprestart generated in the previous step as the new cpin file. This will
> make sure that you don't reset the resstate each time.
>
> Good luck!
> Jason
>
>
>>
>>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Jun 16 2010 - 07:00:04 PDT
